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Nigeria had looked like they would close out victory against South Africa inside 90 minutes on Wednesday, with Troost-Ekong's penalty putting them ahead in the 67th minute.
Victor Osimhen thought he had made it 2-0 with five minutes to go - but in a major twist Bafana Bafana were awarded a penalty for a foul in the build-up to that goal following a Video Assistant Referee review, allowing Teboho Mokoena to equalise.
"It's good VAR because it was a penalty against us," Peseiro conceded.
"But for us, for our minds, it was not good because we were winning 2-0 and then we were drawing 1-1."
Khuliso Mudau almost won it for South Africa in second-half added time before a nervy 30 minutes of extra time and Nigeria's eventual 4-2 triumph on penalties.
"This was a hard one. I think we showed real character," defender Calvin Bassey told BBC Sport Africa.
"It just shows we could do the dirty work. We just had to keep believing in ourselves.
"[South Africa were] a well-organised team, a quality team. To outdo them on penalties, it's crazy.
"Kudos to all the boys that stood up and took [a penalty]. It's not easy to go out there with the pressure and they kept calm."
Goalkeeper Stanley Nwabali was the hero in the shootout for the Super Eagles, denying Mokoena and Evidence Makgopa before Kelechi Iheanacho netted to clinch victory.
"Seeing myself winning the man of the match (award) and also going to the final is a dream come true to me," Nwabali, who plays his club football in South Africa, said.
"Credit to my coaches, because when it's penalty time, they guide me a lot."